Although trained as a chemist, Bauer's interests shifted in the late 1960s from electrochemistry to "science studies," an interdisciplinary mix of history, philosophy, and sociology of science. His special interest is in what he calls "scientific unorthodoxies", like the Loch Ness Monster, Immanuel Velikovsky, and other topics. After retiring from Virginia Tech, Bauer became the editor of the Journal of Scientific Exploration, a publication devoted to fringe and non-mainstream science. He also wrote several books and maintains a website claiming that HIV is not the necessary and sufficient cause of AIDS (a position without scientific support that is known as AIDS denialism).[5]

Bauer was trained as an electrochemist and reported his research in numerous publications during the 1950s and 60s. From the 1970s, although he remained a professor of chemistry in title, Bauer researched fringe science and pseudoscience topics. At Virginia Tech, Bauer was a founding member of a program for science studies, an interdisciplinary mix of history, philosophy, and sociology of science. Bauer's book on science studies, Scientific Literacy and the Myth of the Scientific Method, was reviewed in Science[6] and Nature.[7] In his review in Public Understanding of Science, John Ziman called Bauer "a stalwart veteran" of science studies.[8]

During his investigations of what constitutes pseudoscience, Bauer came to believe in the existence of the Loch Ness Monster, UFOs[9] and other "scientific unorthodoxies". He compares the lack of acceptance of pseudoscientific beliefs by the scientific community to the persecution his family suffered at the hands of the Nazis, stating, "I guess I am kind of naturally contrary....I think you can make a pretty good case that it's not worth just accepting whatever is the standard."[10]

Bauer developed an interest in the Loch Ness Monster and based his belief in the Monster's existence on a film made by prominent “Nessie” enthusiast Tim Dinsdale.[10] The film purportedly shows an object, commonly thought to be a boat, moving in the Scottish lake. In the 1980s, Bauer researched and wrote a book on the Loch Ness Monster and the popular fascination with it. "The Enigma of Loch Ness" was reviewed favorably in Isis.[11] Bauer maintains a website arguing that there is strong evidence for the existence of the monster, which he says the media have conspired to trivialize and sensationalize.[12][13] During his tenure as professor at Virginia Tech, Bauer took over twenty trips to Loch Ness, searching for the monster.[10]

In a news interview, Bauer commented on his belief in the Loch Ness Monster and how it has influenced his career: "I've been quite open about it....if I had been a biologist instead of a chemist, I couldn't have gotten away with it. People could smile and say, 'Well, he's got his hobbyhorse.'"[10]

In his book, Beyond Velikovsky: The History of a Public Controversy, Henry Bauer criticizes the research of Immanuel Velikovsky, author of the pseudoscientific and pseudohistoric New York Times bestseller Worlds in Collision (1950). Time magazine refers to Bauer's book as "the definitive treatise debunking Immanuel Velikovsky."[13] Bauer's book on Velikovsky was reviewed in Science,[14]Nature,[15]ISIS,[16] and Journal for the History of Astronomy.[17]

Bauer says he left the Dean’s office at Virginia Tech "when political correctness arrived" in the 1980s.[2] Bauer joined the National Association of Scholars, a politically conservative advocacy group opposing affirmative action, and started a newsletter for the group's Virginia branch.[18][19] In "The Virginia Scholar," Bauer argues that the implementation of diversity programs led to a decline in academic standards. He characterizes such programs as promoting "feminoid sexists calling men sexist" and "racist black fanatics calling others racist."[18]

Bauer opposed the formation of a police "Sensitive Crime Unit" meant to deal with sexual assault and hate crimes at Virginia Tech, suggesting that these issues were not a serious problem on campus and did not merit special attention. Bauer called the police unit a threat to free speech.[18][20] He criticized Virginia Tech’s creation of a new administrative position for multicultural affairs in response to racial incidents at the university in the mid-1990s as a wasteful allocation of resources. Bauer found fault with Virginia Tech’s policy of excusing student absences for attending religious or ethnic observances. As black enrollment at Virginia Tech declined during the 1990s, Bauer stated that the University was already doing too much ("pulling out all the stops") to attract minority students,[21] and should instead concentrate on raising academic standards.

Bauer also drew criticism for his comments on homosexuality.[22] In his pseudonymously-written memoir To Rise Above Principle: The Memoirs of an Unreconstructed Dean, Bauer writes, "I regard homosexuality as an aberration or illness, not as an ‘equally valid life-style’ or whatever the current euphemism is." In his book, Bauer attributes the perceived problem of homosexuality to genetic, hereditary, and environmental factors, and suggests that the free speech and other civil rights of homosexuals should be withdrawn to prevent what Bauer views as the negative effects of homosexuality from spreading.[23] Bauer has since stated he no longer holds this view, saying he had been "wrong" about the issue and had, in particular, mistakenly relied on the "naturalistic" fallacy that reduced culture and ethics to biology.[24] AIDSTruth.org, an AIDS information resource, notes Bauer posted the statement one day after an account of his views appeared on their website.[22]

Several years after retiring from Virginia Tech, Bauer began to assert that there are "substantive grounds for doubting that HIV is the necessary and sufficient cause of AIDS and that antiretroviral treatment is unambiguously beneficial."[25] In his 2007 book, The Origins, Persistence, and Failings of HIV/AIDS Theory,[26] Bauer questions whether HIV exists, claiming that HIV tests are not accurate and that AIDS death statistics are exaggerated by mainstream media, scientists and pharmaceutical companies.

Bauer’s beliefs on HIV/AIDS are rejected by the mainstream scientific community, based upon the substantial body of research confirming that HIV exists, is infectious, causes AIDS, and that HIV tests are accurate.[27][28]

^The Roanoke Times (report that Bauer addressed a Virginia conference of the Mutual UFO Network): "UFO buffs sighted at lake awhile, then vanish: One in seven people claims to have seen one, but the meeting didn't draw much interest", Jay Conley, Roanoke Times, 28 September 2008. Accessed 28 September 2008.